diff options
Diffstat (limited to 'lib/bbrc.rb')
| -rw-r--r-- | lib/bbrc.rb | 125 |
1 files changed, 62 insertions, 63 deletions
diff --git a/lib/bbrc.rb b/lib/bbrc.rb index 2c2b8a2..1c04a6d 100644 --- a/lib/bbrc.rb +++ b/lib/bbrc.rb @@ -15,6 +15,9 @@ module OpenTox # - get_target Set to "true" to obtain target variable as feature # @return [text/uri-list] Task URI def self.bbrc params + + table_of_elements = [ +"H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn", "Uut", "Fl", "Uup", "Lv", "Uus", "Uuo"] @fminer=OpenTox::Algorithm::Fminer.new @fminer.check_params(params,5) @@ -23,14 +26,13 @@ module OpenTox @bbrc = Bbrc::Bbrc.new @bbrc.Reset - if @fminer.prediction_feature.feature_type == "regression" + if @fminer.prediction_feature.numeric @bbrc.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations! else bad_request_error "No accept values for "\ "dataset '#{@fminer.training_dataset.id}' and "\ - "feature '#{@fminer.prediction_feature.id}'" unless - @fminer.prediction_feature.accept_values - value_map=@fminer.prediction_feature.value_map + "feature '#{@fminer.prediction_feature.id}'" unless @fminer.prediction_feature.accept_values + value_map = @fminer.prediction_feature.accept_values.each_index.inject({}) { |h,idx| h[idx+1]=@fminer.prediction_feature.accept_values[idx]; h } end @bbrc.SetMinfreq(@fminer.minfreq) @bbrc.SetType(1) if params[:feature_type] == "paths" @@ -38,16 +40,18 @@ module OpenTox @bbrc.SetChisqSig(params[:min_chisq_significance].to_f) if params[:min_chisq_significance] @bbrc.SetConsoleOut(false) - feature_dataset = OpenTox::CalculatedDataset.new - feature_dataset.title = "BBRC representatives" - feature_dataset.creator = __FILE__ - feature_dataset.parameters = [ - { "title" => "dataset_id", "paramValue" => params[:dataset].id }, - { "title" => "prediction_feature_id", "paramValue" => params[:prediction_feature].id }, - { "title" => "min_frequency", "paramValue" => @fminer.minfreq }, - { "title" => "nr_hits", "paramValue" => (params[:nr_hits] == "true" ? "true" : "false") }, - { "title" => "backbone", "paramValue" => (params[:backbone] == "false" ? "false" : "true") } - ] + feature_dataset = FminerDataset.new( + :training_dataset_id => params[:dataset].id, + :training_algorithm => "#{self.to_s}.bbrc", + :training_feature_id => params[:prediction_feature].id , + :training_parameters => { + :min_frequency => @fminer.minfreq, + :nr_hits => (params[:nr_hits] == "true" ? "true" : "false"), + :backbone => (params[:backbone] == "false" ? "false" : "true") + } + + ) + feature_dataset.compounds = params[:dataset].compounds @fminer.compounds = [] @fminer.db_class_sizes = Array.new # AM: effect @@ -59,27 +63,32 @@ module OpenTox g_median=@fminer.all_activities.values.to_scale.median #task.progress 10 - step_width = 80 / @bbrc.GetNoRootNodes().to_f - #features_smarts = Set.new + #step_width = 80 / @bbrc.GetNoRootNodes().to_f features = [] - data_entries = Array.new(params[:dataset].compounds.size) {[]} + feature_ids = [] + matches = {} $logger.debug "Setup: #{Time.now-time}" time = Time.now ftime = 0 + itime = 0 + rtime = 0 # run @bbrc - - fminer_results = {} - (0 .. @bbrc.GetNoRootNodes()-1).each do |j| results = @bbrc.MineRoot(j) - #task.progress 10+step_width*(j+1) results.each do |result| + rt = Time.now f = YAML.load(result)[0] - smarts = f[0] - p_value = f[1] + smarts = f.shift + # convert fminer representation into a more human readable format + smarts.gsub!(%r{\[#(\d+)&(\w)\]}) do + element = table_of_elements[$1.to_i-1] + $2 == "a" ? element.downcase : element + end + p_value = f.shift +=begin if (!@bbrc.GetRegression) id_arrs = f[2..-1].flatten max = OpenTox::Algorithm::Fminer.effect(f[2..-1].reverse, @fminer.db_class_sizes) # f needs reversal for bbrc @@ -99,62 +108,52 @@ module OpenTox effect = 'deactivating' end end +=end + rtime += Time.now - rt ft = Time.now - feature = OpenTox::Feature.find_or_create_by({ - "title" => smarts.dup, - "numeric" => true, - "substructure" => true, - "smarts" => smarts.dup, + feature = OpenTox::FminerSmarts.find_or_create_by({ + "smarts" => smarts, "pValue" => p_value.to_f.abs.round(5), - "effect" => effect, - "parameters" => [ - { "title" => "dataset_id", "paramValue" => params[:dataset].id }, - { "title" => "prediction_feature_id", "paramValue" => params[:prediction_feature].id } - ] + #"effect" => effect, + "dataset_id" => feature_dataset.id }) - features << feature + feature_dataset.add_feature feature + feature_ids << feature.id.to_s ftime += Time.now - ft - id_arrs.each { |id_count_hash| - id=id_count_hash.keys[0].to_i - count=id_count_hash.values[0].to_i - fminer_results[@fminer.compounds[id]] || fminer_results[@fminer.compounds[id]] = {} - compound_idx = params[:dataset].compounds.index @fminer.compounds[id] - feature_idx = features.index feature - data_entries[compound_idx] ||= [] - if params[:nr_hits] == "true" - fminer_results[@fminer.compounds[id]][feature] = count - data_entries[compound_idx][feature_idx] = count - else - fminer_results[@fminer.compounds[id]][feature] = 1 - data_entries[compound_idx][feature_idx] = 1 + it = Time.now + f.first.each do |id_count_hash| + id_count_hash.each do |id,count| + matches[@fminer.compounds[id].id.to_s] = {feature.id.to_s => count} end - } + end + itime += Time.now - it - end # end of - end # feature parsing + end + end - $logger.debug "Fminer: #{Time.now-time} (find/create Features: #{ftime})" + $logger.debug "Fminer: #{Time.now-time} (read: #{rtime}, iterate: #{itime}, find/create Features: #{ftime})" time = Time.now - # convert nil entries to 0 - data_entries.collect! do |r| - if r.empty? - Array.new(features.size,0) - else - r[features.size-1] = 0 if r.size < features.size # grow array to match feature size - r.collect!{|c| c.nil? ? 0 : c} # remove nils + n = 0 + feature_dataset.compound_ids.each do |cid| + cid = cid.to_s + feature_dataset.feature_ids.each_with_index do |fid,i| + fid = fid.to_s + unless matches[cid] and matches[cid][fid]# fminer returns only matches + count = 0 + else + count = matches[cid][fid] + end + feature_dataset.bulk << [cid,fid,count] + n +=1 end end - feature_dataset.compounds = params[:dataset].compounds - feature_dataset.features = features - feature_dataset.data_entries = data_entries - $logger.debug "Prepare save: #{Time.now-time}" time = Time.now - #File.open("kazius.json","w+"){|f| f.puts feature_dataset.inspect} + feature_dataset.bulk_write feature_dataset.save $logger.debug "Save: #{Time.now-time}" |